[Chimera-users] fetching EDS files from the web (python script)

Elaine Meng meng at cgl.ucsf.edu
Fri May 31 10:29:21 PDT 2013


Hi Laleh,
If your preferences (Favorites… Preferences, category: Fetch) are set to save files in a download directory, they are already automatically saved locally in a subdirectory named EDS in the download directory.  However, these files are in the .omap  format, not MRC.

Since you can fetch from EDS with the "open" command and write out a map in MRC format with the "volume" command, one possibility is to make a Chimera command script.  Example commands:

open edsID:2fw0
volume #0 save ~meng/Desktop/2fw0.mrc

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>

For combining commands with looping (for example, to process a large set of EDS IDs), see here:
<http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 29, 2013, at 3:10 PM, Laleh <lsoltang at cs.uwaterloo.ca> wrote:

> 
> Hello.
> I'm wondering how I can fetch a bunch of EDS files (from the EDS server) and save them in my local machine in .mrc format. I don't want to do this manually one by one from the user interface... I tried to use open_volume_file with different settings; but it is not working... I'm surprised because this is very starightforward with pdb files. I appreciate your help.
> Thanks in Advance,
> Laleh




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